Secrets of Magica
by Spottedflame of EclipseClan
Summary: Rin Kagamine and Miku Hatsune wake up in the magical city of Mitakihara and begin going to the middle school. As they go to school, they meet Madoka, Homura, and others, and learn more about the secrets of magical girls, maybe even becoming a magical girl themselves...
1. Chapter 1

**Oh hai. So new... Story. Not a oneshot but it won't be a very long story though.**

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The blonde haired female opened her eyes slowly and looked around. Where was she? She didn't recognize this place... Her friend woke up beside her and did the same, showing a shocked expression as she looked around.

"Where are we?" The blonde, Rin, asked her blue haired friend, Miku.

Miku shrugged and stood up with Rin. The sky was cloudless. It almost looked like the ocean at her home. Blue, beautiful, perfect. But she had no idea how to get back to her home. She was in an unfamiliar place and knew no one.

The tree leaves were just starting to change colors, signaling it was almost autumn. She looked at the large building to the left of her. The entire building was almost covered in windows with little building in between. What wall she did she was as white as snow. Stairs led up to brown double doors which she assumed was the front of the building. In the slightly brown grass to the side, there was a sign that said "Mitakihara Middle School". So it was a school.

Miku began walking towards the building and Rin followed closely behind, looking at the unfamiliar area as she walked. Mitakihara. She felt like she heard of this place before. The city... Somehow felt... Magical. She just shrugged it off and walked behind Miku.

There were wooden benches scattered around the school. Multiple students were outside, chatting about school, friends, love letters that were left in their shoe boxes. One girl who stood out from the rest of the students gathered outside was sitting on a bench close to the school alone. She has black hair and wore a black headband. Rin assumed that the clothes she was wearing was the Mitakihara Middle School uniform. It had a black and white skirt and a yellow-white shirt. The skirt had a red stripe near the bottom with small frills. A white section was placed just above the chest area and around the neck area with a black outline. The uniform was finished with a red bow on the small white section.

The black haired student looked up when Miku and Rin approached her.

"Can I help you?" the girl asked.

"Um, we're kind of... Lost. We woke up here and have no idea where we are..." Miku answered, saying almost exactly what Rin would have said.

"Well I'm Homura Akemi. I'm a student at this school."

Rin and Miku introduced themselves and told them their ages—13 and 15—and Homura led them into the school, "Since you're already here, you could enroll in this school." she said, leading them. Rin and Miku both nodded.

Homura stopped at a glass door that had "OFFICE" written on it in large, black letters. They opened the door and walked up the long counter in the room where a young maroon haired woman.

Homura sat in a chair on the other side of the office, waiting for the two to finish. They were both assigned classes. Rin was in class 2-C and Miku was in class 3-A. Homura led Rin to her classroom, which she found out was also Homura's class, and Miku was escorted by the same maroon hairs woman.

Rin was left outside the room while Homura talked to the teacher who nodded at everything. The teacher, who had brown hair, signaled for Rin to come in. She stood in front of the class and introduced herself and slowly wrote her name on the board—Rin Kagamine. The students in the class began to gather around her asking her so many questions she didn't even know where to begin. She was thankful when the bell rung.

Two girls, one with pink hair and one with blue, walked up to Rin with Homura. They introduced themselves as Madoka Kaname and Sayaka Miki. Madoka offered to let Rin and Miku stay at her house, making Rin remember she had no where to stay. She didn't want to burden Madoka by staying at her house but where would she go if she declined? So she accepted and Madoka just smiles cheerfully.

After school, Madoka and Rin found that Miku was waiting outside the school. She was looking at the still perfect sky. Maybe it also reminded her of the ocean at their home. Miku's head turned when she heard footsteps approach her.

"This is Madoka." Rin said, holding out her palm to the pink haired student. "She's going to let us stay at her house."

Miku looked at Rin in a way that told her she was unsure about staying with a person she just met. Though Rin just nodded and Miku shrugged. Madoka smiled slightly and took the lead in front of the other two new students and led them to a large house. Just like the school, it looked like it was covered in windows. A tiny brown-and slightly pink haired boy, maybe around 2 or 3, was playing in the front yard and an older brown haired man, who looked pretty similar to the little kid, was sitting on one of the steps to the front door watching the toddler.

Madoka smiled and ran up to the little boy, pick him up, and spun around, holding him up in the air.

"Madoka! Madoka!" he said cheerfully in a playful voice.

Rin remembered when she and her twin brother were little. They were just innocent kids. But her brother moved to the United States two years ago and she hasn't seen him since.

Miku snapped her out of her thoughts and she realized Madoka was introducing the two people that were outside as well as a new face. She was a woman who had dark pink-red hair. She looked like a business woman. Maybe she was Madoka's mother. Rin didn't know much about her mother as she died when she and her brother were both only 2 years old. They lived with their dad but he never told them anything about their mother.

"This is my mom. She's a business woman. " Madoka said, holding out her palm to the woman, confirming that she was a business woman. "This is my dad. He takes care of our garden in the backyard." Madoka said, standing in front of the older brown haired man. "And my little brother Tatsuya. He's 3 years old and currently goes to kindergarten."

All three of the pink haired female's family nodded and said hello, welcoming both of the girls into their home. The house seemed bigger on the inside than it did on the outside. A kitchen, living room, everything a normal house would have. Every room, combined with the light coming in through all of the windows, made the house look like a pool of sparkles.

Madoka led the two girls into her bedroom. The bed was covered in stuffed animals. The plain white sheets poked out in multiple places. A computer was on the other side of the room on a desk. There was a small lamp sitting on the desk. A small white creature was sitting on the bed in the mix of plushies.

"What _is_ that?" Miku asked, surprised.

Madoka looked surprised herself. Wasn't she supposed to know? When Madoka opened her mouth to reply, nothing came out, leaving the others just as confused as before.

Suddenly, the white creature moved and began to talk. Wait, talk? Wasn't it another plushie?

"I'm Kyuubey! Please to meet you Rin, Miku."

Rin and Miku both looked at each other and silently pointed a finger at themselves.

"H-how do you know our names?" Rin and Miku said in unison.

"I know a lot of things even the smartest humans wouldn't know! So form a contract with me and become a magical girl!"

A magical girl? What's... Going on here?

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**Ah, thank you for reading, I guess. Review if you want. I'll try to post the next chapter as soon as I can.**


	2. Chapter 2

**Ah, so new chapter. Thank you for reading the last chapter. And thank you Gakupo for actually reviewing. You know who you are. xD**

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Rin, Miku, and even Madoka stood in front of the sea of stuffed animals laying on the bed. In the midst of plushies was a small white rabbit-like creature.

"Form a contract with me and become a magical girl!" the creature said without even moving its mouth.

Wait, a magical girl?

Miku turned to Madoka and calmly asked her to explain. So Madoka had Rin and Miku sit down and she began explain the story of magical girls. How the white creature, Kyuubey, would grant any wish and you would become a magical girl to fight off witches. Everything she knew.

"Usually normal humans can't see Kyuubey according to Mami though..." Madoka said, wondering what was wrong. "Well... I guess that means you're not normal humans. Hm..."

Madoka suddenly stood up and grabbed Rin's wrist. She pulled her outside the house with Miku following close behind with a face just as confused as Rin's. A girl, who looked around 14, was outside of Madoka's house, sitting on a tree stump. She stood up as Madoka walked up to her.

"This is Mami Tomoe. She's a veteran magical girl and is also a third year at Mitakihara Middle School." Madoka said calmly.

Miku gasped slightly and her face grew even more surprised. Mami just smiled.

"Y-y-you! You're in my class!" Miku stuttered.

Mami smiled, "Glad you noticed."

The four girls resumed talking about magical girl things. Mami began walking in front of the others while holding on a yellow, shining object.

"This is a Soul Gem. It helps you find where witches are. Witches are what magical girls are meant to fight. They cause despair on the world. They can even cause car wrecks and suicides. If they were near a hospital it wouldn't be good at all." Mami explained.

It was a lot to take it. This magical girl thing seemed to crazy to be real. Maybe she was dreaming? No, she couldn't be...

Mami's Soul Gem began to flash in a strange pattern. Mami smiled slightly, "Well, well. Time to show you what a real witch is like."

Mami held out her Soul Gem in front of her and ribbons spun out from it and wrapped Mami, transforming her into a magical girl outfit. A ribbon appeared on her chest and a feather-like thing on her hat. Her Soul Gem turned into a beam of light and moved up to a flower hair accessory. She held up her hand and colors began to swirl around them. Tiny creatures appeared. They looked like cotton balls with little mustaches. Mami bent back and her chest began to glow and several muskets came out. She pointed one at one of the cotton ball creatures and just as soon as she hit it, it disappeared. She repeated it several times before all of the creatures were gone and they could resume their journey.

Several cotton ball creatures later, the four middle schoolers came to a door with strange letters printed in the middle of it. Mami didn't think about anything and just pushed the door. Inside was a hideous monster. Around it stood several more of the cotton ball creatures.

Madoka looked used to the entire thing. Miku had a disgusted face and Mami just smiled, took a drink of tea, and took off her hat. She spun around with the hat held out from her body and became surrounded in more of her muskets. She held one in both of her hands and began to hit the cotton ball creatures. Once they were gone she started to hit the hideous creature in the center of the room. It made horrible sounding noises every time it was hit by the blonde magical girl.

Rin turned her head for one second to look at Miku with her shocked face. The second Rin looked back, she saw Mami was being held by the witch. Mami just smiled at the girls and turned back around to face the ugly thing.

"I wouldn't want to lose in front of my little students, now would I?" Mami said and shot the witch in the face. It did something that looked similar to wincing and dropped Mami. Ribbons instantly came out from Mami's chest and caught her.

Light formed in front of the third year and a huge gun was formed. Mami grabbed onto it, looking like an ant compared to the thing.

"Tiro... Finale!"

A huge light beam shot from the gun and hit the witch causing it to wither and turn into a puddle of green slime.

Kyuubey stared on with his usual face. Miku looked shocked. Madoka still looked normal, as if she was watching Mami fight against these things for years.

Mami landed elegantly on the ground, holding a cup of tea. She smiles at the other girls like she usually did. She picked up a small black object that was laying on the ground whee the former witch used to be. She suddenly transformed back into the school uniform and the witch's barrier disappeared around them and they were back in the real world. Mami held out her hand to the girls and explained what it was.

"This is a grief seed." Mami said. She held out her Soul Gem. "My Soul Gem looks darker than it did earlier, doesn't it?"

Rin just noticed that Mami's Soul Gem looked slightly darker than before. Before it looked like the sun. Now it's like a light brown color.

"When your Soul Gem is tainted like this, you have to purify it using a grief seed. Witches are the only things to give off a grief seed. Familiars don't give you grief seeds." Mami explained.

Kyuubey chimed in, "A grief seed is a witch egg. Don't worry though, it's safe in this form."

Mami touched her Soul Gem with the grief seed and soon enough her Soul Gem was bright again.

"It should be good for another use." Mami mumbled. She into the shadows near the corner of the room and called, "So I'll give it to you..."

Mami threw the grief seed into the shadows and Rin heard a sound that sounded like someone catching it. The familiar face of Homura came out from the shadows, her hair almost blending in with the dark, shadowy background.

"... Homura Akemi." The blonde puella magi finished.

Homura's face, like when Rin and Miku met her, was expressionless. She stared at the little white creature that sat near Madoka's feet. Kyuubey stared back at the emotionless magical girl, not moving. No sound. Homura broke her stare with Kyuubey and briskly walked up to Madoka, grabbing her wrist and stared into her eyes.

"Remember what I told you, Madoka Kaname. If you value your family and friends, you will not become a magical girl. Please don't, Kaname-san!" Homura's usually cold voice gained a bit of emotion at the end. It was like she knew Madoka like a friend. No, a best friend. So close they could even be family.

Homura wiped away a single stray tear and walked back into the shadows. In an instant, she disappeared like she hadn't even been there. The grief seed laid by Mam

"What was that about, Madoka?" Miku turned to Madoka, wondering what in the world was going on.

Madoka began to explain why Homura said what she did, "Well... On Homura-chan's first day of school at Mitakihara Middle, she had me take her to the nurses office... In one of the empty hallways she told me that if I valued my friends and family and my current way of living, that I shouldn't become a magical girl... And then she left..."

Mami stared into the shadows where the mysterious puella magi disappeared, Rin was spacing out, thinking about what just happened, Madoka was expressionless, while Miku just gritted her teeth...

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**Ah and thank you for reading! Review please!**


	3. Chapter 3

**New chapter. :3 Anyway, not really much to say. Thank you for review if you did. (Again you know who you are.)**

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Miku stood with her teeth gritted and eyes closed. How could that puella magi actually manage to remind her of someone back home? How?

"I guess were done here so we can all go home now." Mami said to the three others.

The girls walked outside of the dark place and separated once they reached the light of the golden, setting sun. Madoka, Rin, and Miku made slow progress back to Madoka's house. They were all thinking about something.

How did Homura remind her so much of her friend? Her childhood friend. Yuki Hiroshi. He was cold and hardly ever talked but once he got used to you, it was hard to get him to stop talking. But then he became sick and died last year. Homura somehow reminded Miku of Yuki. So much that it was almost scary.

When the teal haired girl met Yuki, he was cold and didn't talk much at all. But when around something liked or got used to someone, his voice was full of emotion and happiness.

When Miku looked up, she hadn't realized that they were already in front of the large glass house that belonged to Madoka and her family. The three walked inside and went into Madoka's room along with Kyuubey without a word. By the time everyone calmed down, it was time for them to go to sleep for school the next day. Miku lied in the bed awake and thought about Yuki and her peaceful hometown, almost reliving the horrible moment that she still blamed herself for happening.

_A 14 year old Miku sat next to the snow white hospital bed. The only other person in the room sat in the bed, staring out the window. His almost snow white hair was beginning to grow out in the six months he's been in the hospital. His dark orange eyes didn't have his usual spirit. His skin was extremely pale since he was never allowed outside and could only roam around the eighth floor of the hospital without anything to do._

_He turned his head to looked at the blue haired girl who was lost in her thoughts. She was snapped out of her thoughts when he used to have a voice full of life and cheerfulness but once he was out in the hospital, the life was taken from him and his voice became cold and emotionless once again._

_"Miku. Take me outside."_

_Miku stood up quickly, almost knocking over her chair, "You know you can't go outside, Yuki. The doctor said so. With your illness you just can't or you may..." she said, trailing off at the end._

_Yuki stayed expressionless, looking at her with his dark eyes, "I don't care. I've been inside of this stupid hospital for six months, I have to go outside. I don't care if I get sick. Even if my immune system can't handle things, I don't care. Or... Do you not care about me?"_

_A normal friend would've still denied his request to go outside, knowing it could kill him. But that last sentence made her stop caring. She couldn't bear the thought that Yuki thought she didn't care about him. So she grabbed him pale hand and helped him out of the bed and snuck him outside to satisfy his need to see the outside world for the first time in months._

_Once they made it into the empty elevator, they both let out a sigh of relief. Luckily, they didn't stop on another floor until they made it to the first floor, and the doors to the world that Yuki hasn't seen in forever._

_Yuki tried adjusting to the air, the pollen, and everything around him in the area full of blooming plants and hyper animals. The sounds of the people coming and going out of the large, well known hospital were almost too much to bear. Miku knew that if it was bad for her then it was bad for Yuki._

_Yuki coughed a couple times. With each cough a spark of life came to his eyes and quickly disappeared right after. His slight cough turned into a coughing fit, extremely deadly for Yuki. Who knows how strong his body was for that. She... Wouldn't be able to forgive herself if he... Died._

_The white haired boy's coughing fit gave them a few stares from the many people around them. A nurse dressed in white clothes rushed outside and grabbed Yuki, leaving the wheelchair and the blue haired girl behind. Miku dropped to the ground and buried her face within her hands. She knew he wasn't strong enough to go outside. But she couldn't let him think that she didn't care about him! That would be worse then never seeing him again..._

_Miku slowly stood up, trying to recover from her little scene. Dragging her feet, she walked inside and asked the lady behind the counter where her childhood friend was. Room 102. Emergency._

_She walked as fast as she possibly could without running to the small room in the back of the hallway. Room 102 was printed on the door in large black letters. Below it was the word emergency, also written in black letters, but slightly smaller than the room number. She had to force herself not to slam the double doors open. Yuki couldn't die! He just couldn't!_

_She sat in the dark blue plastic chair next to the bed Yuki lied in. Monitors and IVs were hooked up to him._

_"I'm sorry..." she whispered to herself, "I'm so sorry, Yuki. You're... Going to be okay."_

_As soon as the last word came tumbling out of her mouth, the heart monitor started beeping and triggered tears to start flowing down her face._

_"Yuki..." Miku whispered to herself as quietly as she could._

_Miku spaced out and never heard the doctors rush in, trying to make his heart start beating again. They messed with every machine in the room. Yuki's orange eyes looked like glass, nothing. They were worse than that stare she got from Yuki with his emotionless eyes. There was nothing. She put her hand over his eyes and gently closed them._

_She couldn't bear to stay in that room anymore. He was gone. And he'll never come back._

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**Aha, review if you like!**


	4. Chapter 4

**Oh hai. New chapter once again. I swear this is probably the first time I've actually updated this much. xD Guys guys, I get to go see the third Madoka Magica movie in theaters. I'm so happy.**

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Rin woke up, expecting light to be shining in through the window, but only woke up to the darkness of the room. It was probably the middle of the night so she would have to be extremely careful as to not wake up Madoka or Miku. Her eyes moved across the room, her eyes already adjusted to the darkness, until her gaze landed on the futon lying close to Madoka's bed where Miku should be sleeping.

Where was she?

Rin quietly got up, not wanting to wake up her new pink haired friend when opening the door. She went down the stairs and into the kitchen but no one was there. Not even Madoka's mother Junko who was usually up late drinking. But it was empty and so were the other rooms Miku could be in.

Rin went back into Madoka's room and decided whether she should wake up Madoka. She decided against it and just grabbed a jacket and went outside to look for Miku.

The air was slightly cold, letting Rin know that autumn was almost here. She had her hands in her pockets and looked around, holding her hair out of her face. A bright glow shined in the distance, catching Rin's attention. She made her way to the bright shine and found Miku and Kyuubey standing next to a park bench.

Rin hid behind a tree in case Miku would consider her an unwelcome guest at the time.

Kyuubey began to speak to Miku, once again his mouth not moving, "You can make one wish, any wish at all, to form a contract and become a magical girl. No matter how impossible it may seem, your wish will come true."

Miku nodded and closed her teal colored eyes, "I wish that Yuki Hiroshi, my best friend, to be alive again and live here in Mitakihara."

Kyuubey sat still until a teal ball of light came out of Miku's chest, which appeared to cause a lot of pain for the teal haired girl.

"Now, embrace it." Kyuubey said.

Miku clasped her hands around the shining ball and when she opened them again, it had formed into what Rin recognized as a Soul Gem.

Rin watched the transformation of Miku from girl to magical girl. Sparkles of every color—pink, blue, red, yellow—formed around the teal haired girl and wrapped around her like a sparkly cocoon. When every sparkle was gone, the only thing left was Miku in her magical girl outfit. She looked at herself but quickly transformed back to her normal form. And the next thing she knew, Yuki appeared from behind a tree.

"Miku?" Yuki said, looking around at the unfamiliar place he suddenly appeared in.

Miku's head turned, her eyes held mixed emotions, sadness, happiness, surprise. It was like she wasn't sure if Kyuubey could actually grant her wish.

"Where am I?" Yuki walked up to Miku, still looking around.

"We're in the magical city of Mitakihara, Yuki." Miku answered.

"Magical?"

Miku had no time to answer before Madoka ran up to them, coming from the direction of her house. They all gathered and headed back to her house. Rin, hidden among the many shadows, followed them.

Back at Madoka's house, they all settled down. Yuki and Miku stayed up talking for a while until Yuki went to sleep and Miku laid on her futon, looking at her bright teal Soul Gem. Rin stood up and walked over to her.

"Can I... Talk to you outside. I don't want to wake anyone up." Rin whispered to the new puella magi.

Miku and nodded and the two headed downstairs and sat outside, near the garden Madoka's father was in when Madoka brought them to her home. Rin turned to Miku and took a deep breath, then hugged her, her tears finally coming out.

"Miku... I don't want anything to happen to you. So don't do anything reckless... Okay?" Rin said, forcing herself to steady her voice as much as possible while she was crying.

Miku only stared into the distance, surprised by the sudden hug from her friend.

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**Pretty short compared to the others, sorry. Review if you want.**


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